The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

Mukhopadhyay, Rituparna; Yu, Wenqiang; Whitehead, Joanne; Xu, JunWang; Lezcano, Magda; Pack, Svetlana D.; Kanduri, Chandrasekhar; Kanduri, Meena; Ginjala, Vasudeva; Vostrov, Alexander A.; Quitschke, Wolfgang; Chernukhin, Igor; Klenova, Elena; Lobanenkov, Victor; Ohlsson, Rolf

doi:10.1101/gr.2408304

Cited by 126 publications

(122 citation statements)

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“…Insulators, for example, are needed to keep genes in silent domains, away from the influence of neighboring enhancers. The prototypical insulator from the chicken ␤-globin locus contains binding sites for the 11-zinc-finger protein CTCF, and binding of CTCF is necessary for insulator function, not only in the chicken but also in many mammalian insulators (1)(2)(3)(4). How CTCF confers chromatin insulation is not clear, but recent work shows that DNA-bound CTCF molecules can dimerize in a binding site-specific fashion (5) and that CTCF binds nucleophosmin and may be tethered to the nuclear matrix (6).…”

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confidence: 99%

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

Kurukuti

Tiwari²,

Tavoosidana³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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It is thought that the H19 imprinting control region (ICR) directs the silencing of the maternally inherited Igf2 allele through a CTCFdependent chromatin insulator. The ICR has been shown to interact physically with a silencer region in Igf2, differentially methylated region (DMR)1, but the role of CTCF in this chromatin loop and whether it restricts the physical access of distal enhancers to Igf2 is not known. We performed systematic chromosome conformation capture analyses in the Igf2͞H19 region over >160 kb, identifying sequences that interact physically with the distal enhancers and the ICR. We found that, on the paternal chromosome, enhancers interact with the Igf2 promoters but that, on the maternal allele, this is prevented by CTCF binding within the H19 ICR. CTCF binding in the maternal ICR regulates its interaction with matrix attachment region (MAR)3 and DMR1 at Igf2, thus forming a tight loop around the maternal Igf2 locus, which may contribute to its silencing. Mutation of CTCF binding sites in the H19 ICR leads to loss of CTCF binding and de novo methylation of a CTCF target site within Igf2 DMR1, showing that CTCF can coordinate regional epigenetic marks. This systematic chromosome conformation capture analysis of an imprinting cluster reveals that CTCF has a critical role in the epigenetic regulation of higher-order chromatin structure and gene silencing over considerable distances in the genome.genomic imprinting ͉ insulators ͉ chromosome biology A variety of control elements, such as enhancers, silencers, and chromatin insulators, are thought to establish and maintain domains of gene expression or repression in the genome. Insulators, for example, are needed to keep genes in silent domains, away from the influence of neighboring enhancers. The prototypical insulator from the chicken ␤-globin locus contains binding sites for the 11-zinc-finger protein CTCF, and binding of CTCF is necessary for insulator function, not only in the chicken but also in many mammalian insulators (1-4). How CTCF confers chromatin insulation is not clear, but recent work shows that DNA-bound CTCF molecules can dimerize in a binding site-specific fashion (5) and that CTCF binds nucleophosmin and may be tethered to the nuclear matrix (6). CTCF emerges, therefore, as a potential mediator of long-range interactions that are involved in establishing repressed domains.Regional coordination of gene expression and repression is found in many imprinted gene clusters in the mammalian genome and is regulated by imprinting centers or imprinting control regions (ICRs) (7-10). A well characterized cluster is that containing the paternally expressed Igf2 and maternally expressed H19. Both genes share enhancers, and the ICR is located in the 5Ј flank of the H19 gene (11). The deletion of this ICR results in biallelic expression of both Igf2 and H19, demonstrating a role of the ICR to repress the maternal Igf2 allele, which is located Ͼ80 kb away (12). The mechanism underlying this function has been proposed to involve a CTCF-dependent...

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confidence: 99%

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

Kurukuti

Tiwari²,

Tavoosidana³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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482

420

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“…CTCF silences genes by binding to sites within promoters, silencers, and insulators through the use of different combinations of zinc fingers (20). More than 15,000 CTCFbinding sites have been identified throughout the genome (16).…”

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confidence: 99%

CTCF Regulates Allelic Expression of Igf2 by Orchestrating a Promoter-Polycomb Repressive Complex 2 Intrachromosomal Loop

Qiu

et al. 2008

Molecular and Cellular Biology

175

193

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CTCF is a zinc finger DNA-binding protein that regulates the epigenetic states of numerous target genes. Using allelic regulation of mouse insulin-like growth factor II (Igf2) as a model, we demonstrate that CTCF binds to the unmethylated maternal allele of the imprinting control region (ICR) in the Igf2/H19 imprinting domain and forms a long-range intrachromosomal loop to interact with the three clustered Igf2 promoters. Polycomb repressive complex 2 is recruited through the interaction of CTCF with Suz12, leading to allelespecific methylation at lysine 27 of histone H3 (H3-K27) and to suppression of the maternal Igf2 promoters. Targeted mutation or deletion of the maternal ICR abolishes this chromatin loop, decreases allelic H3-K27 methylation, and causes loss of Igf2 imprinting. RNA interference knockdown of Suz12 also leads to reactivation of the maternal Igf2 allele and biallelic Igf2 expression. CTCF and Suz12 are coprecipitated from nuclear extracts with antibodies specific for either protein, and they interact with each other in a two-hybrid system. These findings offer insight into general epigenetic mechanisms by which CTCF governs gene expression by orchestrating chromatin loop structures and by serving as a DNA-binding protein scaffold to recruit and bind polycomb repressive complexes.The transcriptional regulator CCCTC-binding factor (CTCF) is a highly conserved 11-zinc-finger nuclear protein that controls the expression of a number of genes via chromatin insulation or enhancer blocking (for reviews, see references 5, 8, 23, and 28). CTCF silences genes by binding to sites within promoters, silencers, and insulators through the use of different combinations of zinc fingers (20). More than 15,000 CTCFbinding sites have been identified throughout the genome (16).The role of CTCF as an insulator regulating the imprinting of Igf2 and H19 has been extensively studied. Igf2 and H19 imprinting is directed by epigenetic modifications in the differentially methylated region (DMR) of the imprinting control region (ICR) located between these two adjacent genes (1,9,19,21,29,30). The binding of CTCF to the unmethylated maternal ICR creates a physical boundary, blocking the interaction of downstream enhancers with the remote Igf2 promoters and silencing the maternal allele (4,13,15). When this ICR is deleted (35) or mutated (32, 34), the maternal Igf2 allele is expressed, leading to biallelic expression. In addition, CTCF has recently been shown to act as a tethering protein, serving as a molecular glue to secure long-range intrachromosomal (17) and interchromosomal (18) interactions.By chromosome configuration capture (3C) methodology, it has been shown that CTCF participates in the formation of a long-range chromosomal loop to the upstream Igf2 DMRs when it is bound to the maternal ICR (17,42,21). This model suggests that CTCF may not only function as a physical insulator but also actively participate in the regulation of the imprinted Igf2 allele. We were interested in learning how CTCF mediates the suppressi...

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“…This process requires complex molecular mechanisms including the participation of multiple cytokines, growth factors, adhesion factors and proteases (Lash et al, 2006;Mihaljevic et al, 2010;Nerlich et al, 2009;Wong and Gumbinger, 2003). Through wide-scale screening for CTCF binding site by CHIP, CTCF might also regulate the expression of proteins similar to cadherin like 26 and MMP23B (Arpanahi et al, 2009;Mukhopadhyay et al, 2004). Cadherin plays a role in adhesion between cells or between cells with ECM.…”

Section: Discussionmentioning

confidence: 99%

CCCTC-Binding Factor Controls Its Own Nuclear Transport via Regulating the Expression of Importin 13

Wang¹,

Shen²,

Huang³

et al. 2013

Molecules and Cells

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The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

Cited by 126 publications

References 24 publications

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

CTCF Regulates Allelic Expression of Igf2 by Orchestrating a Promoter-Polycomb Repressive Complex 2 Intrachromosomal Loop

CCCTC-Binding Factor Controls Its Own Nuclear Transport via Regulating the Expression of Importin 13

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